Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi18g670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g671 . . . . . Bpe04g00162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g672 . . . . . . . . Cmo05g00151 Cmo12g00526 . . . . . . Cpe07g00510 Bhi04g00404 . . . . . Lcy13g2125 . . . . . . . . . . . . . . Cme03g02092 . . . . . Bpe05g00038 . Bma05g00049 . . . Cma12g00589 Cma05g00150 . . . . . . . . . . . . . . . . . . . Csa02g01905 Chy03g01581 .
Vvi18g673 Blo01g01499 . Bda01g00583 . Bpe02g00447 . . Bma01g02253 . Cmo12g00524 . . . . Sed11g0923 . Cpe07g00509 Bhi04g00403 Tan02g1758 Cmetu03g1631 . Hepe08g1321 . Lcy13g2124 Cla08g01610 Cam08g2111 Cec08g1696 Cco08g1820 Clacu08g1796 . Cre08g1579 . . Cone17ag0876 Cone20ag0224 . . . Cme03g02091 . . . . . . . . . . . Cma12g00587 . . . . . . . . . . . . . . . . . . . Lsi08g01514 Csa02g01906 Chy03g01580 .
Vvi18g674 . . . . . . . . Cmo05g00152 Cmo12g00523 . . . . Sed11g0927 . Cpe07g00508 Bhi04g00402 Tan02g1760 Cmetu03g1564 . Hepe08g1320 . Lcy13g2123 Cla08g01609 Cam08g2110 Cec08g1695 Cco08g1819 Clacu08g1795 . Cre08g1578 Cone4ag1608 Cone7ag1344 Cone17ag0875 Cone20ag0223 . . . Cme03g02090 Blo17g00868 Blo18g00713 . Bda01g01595 Bpe02g01782 Bpe05g00037 Bma01g00672 Bma05g00048 . . . Cma12g00586 Cma05g00152 Car05g00132 . Cpe11g00128 . . . . . . . . . . . . . . . Lsi08g01513 Csa02g01907 Chy03g01579 .
Vvi18g675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g677 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g678 Blo01g01500 . Bda01g00582 . . . . . . . Cma01g01798 Cma09g00274 Car01g01404 . . . . . . . . . . . . . . . . . . . . . . Lsi04g01501 . . . . . . . . . . . Sed13g1794 Cmo01g01857 Cmo09g00270 . . . Car09g00229 . Cpe02g00210 Bhi09g03248 Tan01g4716 Cmetu04g1405 . Hepe01g1814 Mch11g0346 . Cla05g02092 Cam05g2245 Cec05g2264 Cco05g2305 Clacu05g2242 Cmu05g2105 Cre05g2228 . . . .
Vvi18g679 . . . . . . . . Cmo05g00153 . . . . . Sed10g1211 . . Bhi04g00400 Tan02g1762 Cmetu03g0353 . Hepe08g1319 . Lcy13g2122 Cla08g01608 Cam08g2109 Cec08g1694 Cco08g1818 Clacu08g1794 . Cre08g1577 . . Cone17ag0873 Cone20ag0221 . . . Cme03g02087 . . . . . . . . . . . Cma12g00585 Cma05g00153 Car05g00133 . Cpe11g00129 . . . . . . . . . . . . . . . Lsi08g01512 Csa02g01908 Chy03g01578 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32855040 32856364 + Bda002602.2 Bda01g00582 582
1 32859752 32861391 + Bda002603.1 Bda01g00583 583
1 51785736 51787578 + Bda003865.1 Bda01g01595 1595
4 10445540 10447760 + XM_039030332.1 Bhi04g00400 400
4 10462100 10466028 - XM_039029172.1 Bhi04g00402 402
4 10466705 10469132 + XM_039029173.1 Bhi04g00403 403
4 10469685 10472546 - XM_039029170.1 Bhi04g00404 404
9 83325526 83327190 - XM_039043998.1 Bhi09g03248 3248
1 54564865 54566538 - BLOR01499 Blo01g01499 1499
1 54569207 54570512 - BLOR01500 Blo01g01500 1500
17 28374940 28384877 + BLOR08414 Blo17g00868 868
18 17270358 17272245 - BLOR09201 Blo18g00713 713
1 6129301 6131029 - Bma000882.1 Bma01g00672 672
1 79693726 79695364 - Bma003106.1 Bma01g02253 2253
5 2330285 2332438 - Bma020737.1 Bma05g00048 48
5 2336507 2338801 - Bma020738.1 Bma05g00049 49
2 2925786 2927412 + Bpe008288.2 Bpe02g00447 447
2 20122679 20124406 + Bpe009614.1 Bpe02g01782 1782
4 1052484 1054057 + Bpe014880.1 Bpe04g00162 162
5 718776 720295 - Bpe017424.1 Bpe05g00037 37
5 723973 726261 - Bpe017425.1 Bpe05g00038 38
5 30653268 30654541 + CaPI482276_05g022450.1 Cam05g2245 2245
8 26533484 26535943 + CaPI482276_08g021090.1 Cam08g2109 2109
8 26538507 26541944 - CaPI482276_08g021100.1 Cam08g2110 2110
8 26542409 26544300 + CaPI482276_08g021110.1 Cam08g2111 2111
1 12211137 12212893 - Carg10633-RA Car01g01404 1404
5 663374 666322 + Carg11872-RA Car05g00132 132
5 666683 668494 - Carg11871-RA Car05g00133 133
9 1286325 1287000 + Carg21792-RA Car09g00229 229
5 31668067 31669576 + CcPI632755_05g023050.1 Cco05g2305 2305
8 29233458 29235699 + CcPI632755_08g018180.1 Cco08g1818 1818
8 29238301 29241690 - CcPI632755_08g018190.1 Cco08g1819 1819
8 29242155 29244093 + CcPI632755_08g018200.1 Cco08g1820 1820
5 34039994 34041266 + CePI673135_05g022640.1 Cec05g2264 2264
8 28141707 28144166 + CePI673135_08g016940.1 Cec08g1694 1694
8 28148030 28151445 - CePI673135_08g016950.1 Cec08g1695 1695
8 28151910 28153874 + CePI673135_08g016960.1 Cec08g1696 1696
3 17852472 17854283 + Chy3G065580.1 Chy03g01578 1578
3 17856794 17859731 - Chy3G065590.1 Chy03g01579 1579
3 17860180 17862165 + Chy3G065600.1 Chy03g01580 1580
3 17863086 17865404 - Chy3G065610.1 Chy03g01581 1581
5 30856591 30857864 + ClG42_05g0224200.10 Clacu05g2242 2242
8 27286332 27288793 + ClG42_08g0179400.10 Clacu08g1794 1794
8 27291348 27294783 - ClG42_08g0179500.10 Clacu08g1795 1795
8 27295248 27297166 + ClG42_08g0179600.10 Clacu08g1796 1796
5 32546919 32548663 + ClCG05G020410.1 Cla05g02092 2092
8 28707044 28708852 + ClCG08G016330.1 Cla08g01608 1608
8 28712351 28715869 - ClCG08G016340.2 Cla08g01609 1609
8 28715998 28718234 + ClCG08G016350.1 Cla08g01610 1610
1 12005164 12006799 - CmaCh01G017980.1 Cma01g01798 1798
5 661618 663927 + CmaCh05G001500.1 Cma05g00150 150
5 665069 668371 + CmaCh05G001520.1 Cma05g00152 152
5 668864 670621 - CmaCh05G001530.1 Cma05g00153 153
9 1134569 1136209 + CmaCh09G002740.1 Cma09g00274 274
12 3060856 3061509 + CmaCh12G005850.1 Cma12g00585 585
12 3061750 3065341 - CmaCh12G005860.1 Cma12g00586 586
12 3066141 3068369 + CmaCh12G005870.1 Cma12g00587 587
12 3069290 3071554 - CmaCh12G005890.1 Cma12g00589 589
3 28242971 28244782 + MELO3C010820.2.1 Cme03g02087 2087
3 28246692 28250791 - MELO3C010819.2.1 Cme03g02090 2090
3 28250235 28252523 + MELO3C010818.2.1 Cme03g02091 2091
3 28252992 28255565 - MELO3C010817.2.1 Cme03g02092 2092
3 1083259 1085067 - PI0002416.1 Cmetu03g0353 353
3 1077409 1081069 + PI0024161.1 Cmetu03g1564 1564
3 1074686 1077364 - PI0025808.1 Cmetu03g1631 1631
4 21415749 21417012 - PI0007030.1 Cmetu04g1405 1405
1 13503775 13505613 - CmoCh01G018570.1 Cmo01g01857 1857
5 663324 665645 + CmoCh05G001510.1 Cmo05g00151 151
5 666796 670085 + CmoCh05G001520.1 Cmo05g00152 152
5 670507 672264 - CmoCh05G001530.1 Cmo05g00153 153
9 1188570 1191514 + CmoCh09G002700.1 Cmo09g00270 270
12 3216344 3219880 - CmoCh12G005230.1 Cmo12g00523 523
12 3221711 3223942 + CmoCh12G005240.1 Cmo12g00524 524
12 3224994 3227282 - CmoCh12G005260.1 Cmo12g00526 526
5 30591109 30592382 + CmPI595203_05g021050.1 Cmu05g2105 2105
4 12218257 12220582 - Conep04aG0166000.1 Cone4ag1608 1608
7 9787013 9789335 + Conep07aG0138500.1 Cone7ag1344 1344
17 6923857 6925856 + Conep17aG0089300.1 Cone17ag0873 873
17 6933724 6936293 - Conep17aG0089500.1 Cone17ag0875 875
17 6936442 6937903 + Conep17aG0089600.1 Cone17ag0876 876
20 947456 949491 + Conep20aG0023100.1 Cone20ag0221 221
20 956217 957016 - Conep20aG0023300.1 Cone20ag0223 223
20 957494 958901 + Conep20aG0023400.1 Cone20ag0224 224
2 1078945 1080813 + Cp4.1LG02g06610.1 Cpe02g00210 210
7 3337673 3339679 - Cp4.1LG07g04970.1 Cpe07g00508 508
7 3340700 3343296 + Cp4.1LG07g05040.1 Cpe07g00509 509
7 3344112 3346400 - Cp4.1LG07g04920.1 Cpe07g00510 510
11 701061 709372 + Cp4.1LG11g01280.1 Cpe11g00128 128
11 709751 711562 - Cp4.1LG11g01380.1 Cpe11g00129 129
5 33920546 33921818 + CrPI670011_05g022280.1 Cre05g2228 2228
8 28336995 28339452 + CrPI670011_08g015770.1 Cre08g1577 1577
8 28342066 28345520 - CrPI670011_08g015780.1 Cre08g1578 1578
8 28345985 28347909 + CrPI670011_08g015790.1 Cre08g1579 1579
2 18004320 18007286 + CsaV3_2G026250.1 Csa02g01905 1905
2 18007655 18009909 - CsaV3_2G026260.1 Csa02g01906 1906
2 18010062 18013370 + CsaV3_2G026270.1 Csa02g01907 1907
2 18014716 18017625 - CsaV3_2G026280.1 Csa02g01908 1908
1 83117636 83123222 + Hsped.01g18140.1 Hepe01g1814 1814
8 15019772 15021406 + Hsped.08g13190.1 Hepe08g1319 1319
8 15023518 15028839 - Hsped.08g13200.1 Hepe08g1320 1320
8 15037212 15040159 + Hsped.08g13210.1 Hepe08g1321 1321
13 40131151 40132896 + Maker00025444 Lcy13g2122 2122
13 40136129 40140729 - Maker00025334 Lcy13g2123 2123
13 40141443 40143826 + Maker00025287 Lcy13g2124 2124
13 40144800 40147127 - Maker00025357 Lcy13g2125 2125
4 22676331 22678250 - Lsi04G015010.1 Lsi04g01501 1501
8 23211820 23213535 + Lsi08G015120.1 Lsi08g01512 1512
8 23216809 23220482 - Lsi08G015130.1 Lsi08g01513 1513
8 23221197 23223680 + Lsi08G015140.1 Lsi08g01514 1514
11 2147984 2149932 + MC11g0269 Mch11g0346 346
10 25176921 25178937 - Sed0011842.1 Sed10g1211 1211
11 22956504 22959218 - Sed0004073.1 Sed11g0923 923
11 22960046 22963215 + Sed0010091.4 Sed11g0927 927
13 22982455 22984163 + Sed0020836.1 Sed13g1794 1794
1 113027455 113029195 - Tan0004751.1 Tan01g4716 4716
2 81565854 81568422 - Tan0019892.1 Tan02g1758 1758
2 81570628 81577848 + Tan0011433.2 Tan02g1760 1760
2 81650138 81651907 - Tan0010659.1 Tan02g1762 1762
18 7836871 7838406 + Vvi18g670 Vvi18g670 670
18 7839601 7843143 + Vvi18g671 Vvi18g671 671
18 7846236 7853155 + Vvi18g672 Vvi18g672 672
18 7855775 7862786 - Vvi18g673 Vvi18g673 673
18 7866960 7871581 + Vvi18g674 Vvi18g674 674
18 7874252 7878811 + Vvi18g675 Vvi18g675 675
18 7880353 7881001 - Vvi18g676 Vvi18g676 676
18 7881955 7888602 - Vvi18g677 Vvi18g677 677
18 7890139 7891713 - Vvi18g678 Vvi18g678 678
18 7895437 7897711 - Vvi18g679 Vvi18g679 679
       

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